I also had the same problem trying to use amber files with 2.7b2. I
had a cursory look at the code and it seems that the problem is the
variable numenerentries (Parameteres.C), which is never initialized
when reading amber parameters.

in the constructor for reading amber parameter data did the job (i.e.
a simple test run gives the same results using b2 and b1)

*Beware* that I'm not sure if this is a proper solution or if on the
contrary it breaks something else (I'm using namd only since a couple
of days, and I don't know the internals: mine is just a wild guess) so
use it at your own risk...

Maybe somebody else could check this?

Cheers,

Marcello

On Wed, Mar 31, 2010 at 2:02 PM, Vlad Cojocaru <Vlad.Cojocaru_at_h-its.org> wrote:
> Dear Peter,
>
> I did not have the time to further test new CVS codes but if you still have
> the problem with the newest CVS codes .. I am afraid that the problem is not
> fixed yet.
> I post my reply to the list as well maybe there are some updates from the
> NAMD developers on this .. Of course, this problem is a very important one
> for everybody who is using NAMD with AMBER ff ..
>
> Cheers
> Vlad
>
> Peter Schmidtke wrote:
>>
>> Dear Vlad,
>>
>> I saw your posts on the namd mailing list and wondered if you finally
>> solved the problem, I have the same right now and I did not find any
>> follow
>> up of the problem on the namd mailing list.
>> The amber ff part of my conf file looks like this :
>>
>> amber on
>> parmfile ../s_comp1.top
>> ambercoor ../s_comp1.crd
>> outputname s_comp1_min
>> exclude scaled1-4
>> 1-4scaling 0.833333
>>
>> where s_comp1.top is a amber topology, and the crd file is an amber
>> coordinate file. Like in your case it yields a segmentation fault during
>> the starting phase.
>>
>> Thanks in advance for your help
>>
>> Best regards.
>>
>>
>>
>
> --
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> Dr. Vlad Cojocaru
>
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>
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>
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